Biochemical Pathways Workbench

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The University of California-San Diego is awarded a grant to develop a comprehensive pathways database, query/analysis toolkit, interface infrastructure, and an authoring toolkit, called Biochemical Pathways Workbench (BPW) for biological networks. The goal of this Workbench is to provide scientists with a computational sandbox in which they can develop complex applications, or choose from an extensive set of analysis tools provided by the database. The project targets fundamental contributions in biological modeling, algorithm design, analytical modeling, statistical validation, and deployment into the existing Biology Workbench (http://workbench.sdsc.edu). The project will be a collaborative effort with Purdue University.Traditional data repositories provide interfaces to sequence and structure-based annotations. Given the emerging trend in biology towards pathways, networks, and systems, there is a need to provide data, analysis, and modeling interfaces to pathways. We will provide such an interface to various data sources from biochemical pathways and enhance these with data and applications from our own laboratory. The tool will offer interoperability with other data sources including sequence and expression databases, support an API using which programmers will be able to transparently query remote databases, and provide a graphical interface to its analysis tools in the form of an authoring toolkit. Using this toolkit, scientists will be able to experiment with diverse data sources integrated into BPW networks and databases. The infrastructure in an open architecture will be integrated into the Biochemical Pathways WorkBench, and made available to the broader science and education community. The project will invest considerable effort during the second year to develop instructional media courses at UCSD and Purdue that demonstrate the educational value of the tool.